Main
Rui Fu
RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus
I have studied various aspects of RNA-related gene expression regulation processes, including transcription, translation, and especially RNA degradation. In lieu of 10 years of bench research experience, I have now worked several years in bioinformatic roles analyzing high throughput sequencing data.
Education
Ph.D. Biological Science
University of California San Diego
La Jolla, CA
2015 - 2009
B.S. Biological Science
Xiamen University
Xiamen, China
2009 - 2005
Research Experience
Bioinformatic tool development: 1) clustifyr, single cell RNA-seq cell identity assignment (author); 2) valr, tidyverse-style genomic interval analysis (co-developer); 3) scraps, extraction of polyadenylation site info from scRNA-seq data (co-developer); 4) squirrelBox, RNA-seq data visualization and analysis browser using Shiny (author)
Postdoctoral Informatics Fellow
Jay Hesselberth’s Supervision
University of Colorado Anschutz
Current - 2017
- Development of bioinformatics software packages
- RNA-seq and transcriptome improvements for hiberating ground squirrel brain regions
- Informatics support on various RNA biology collaborations, analyzing genomic and sequencing data
Postdoctoral Research Fellow
Judy Lieberman’s Lab
Harvard Medical School
2017 - 2016
- Identification of the mitochondrial trigger of apoptotic mRNA decay
- Purificiation of cytotoxic granules and key cytolytic molecules by fast protein liquid chromatography
- Mouse gene manipulation by CRISPR-Cas9, and genotyping with R scripts
Graduate Research Assistant
Jens Lykke-Andersen’s Lab
University of California San Diego
2015 - 2009
- Investigation of co-factors involved in ZFP36(TTP)-mediated mRNA decay and translational repression during the immune response of macrophages
- Characterization of the roles of ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts
Undergraduate Research Assistant
Ruichuan Chen’s Lab
Xiamen University
2009 - 2007
- Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
- Mechanistic characterization of p-TEFb activation by HIV-Tat
Teaching Experience
Lecture Instructor (Graduate Level Courses)
University of Colorado Anschutz
N/A
Current - 2018
- Lecture for RNA sequencing section of Rigor in Research (2020)
- Lectures, paper discussion, and exam/homework design for RNA section of Foundations in Biomedical Sciences (2018, 2019)
- Lectures for Practical Data Analysis with R/RStudio (2018, 2019)
- Workshop for scRNA-seq Data Analysis (2019)
Teaching Assistant (Graduate Level Courses)
University of Colorado Anschutz
N/A
Current - 2019
- Practical Computational Biology for Biologists: R
- Practical Computational Biology for Biologists: Python
RNA Bioscience Initiative Informatics Office Hour (weekly)
University of Colorado Anschutz
N/A
Current - 2018
RNA Bioscience Initiative Summer Internship Mentoring
University of Colorado Anschutz
N/A
2020
- Mentoring of undergraduate summer research, systemically exploring scRNA-seq cell type signatures
Summer Research Mentoring
Harvard Medical School
N/A
2017
- Mentoring of bench/informatics research and scientific writing for high school student enrolled in the MIT Research Science Institute program
BS/MS Student Research Mentoring
University of California San Diego
N/A
2015 - 2013
- Mentoring of student research for undergraduate honor thesis and master thesis projects
- Mentee was awarded best poster presentation at 2014 Biological Sciences Annual Student Research Showcase
Teaching Assistant (Undergraduate)
University of California San Diego
N/A
2012 - 2011
- Molecular Biology
- DNA Recombination Lab
Posters and Talks
ClustifyR: automated single-cell RNA sequencing cluster classification
Keystone Symposia on Single Cell Biology (Poster)
N/A
2019
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis
Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2017
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis
2016 Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2016
TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex
Cold Spring Harbor Laboratory mRNA Processing Meeting (Presentation)
N/A
2015
TTP represses translation of target mRNAs through the 4EHP-GYF2 complex
UCSD Mechanisms of Gene Expression Seminar (Presentation)
N/A
2014
TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition
Cold Spring Harbor Laboratory mRNA Processing Meeting (Poster)
N/A
2013
The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression
Keystone Symposia on Protein-RNA Interactions (Poster)
N/A
2012
Service, Training, Recognition
Society memberships: RNA Society, International Society for Computational Biology, Genetics Society of America
GENETICS Early Career Reviewer
N/A
N/A
Current - 2018
Peer review of manuscripts under Dr Lykke-Andersen, Dr Lieberman, Dr Hesselberth
N/A
N/A
Current - 2011
Admissions Committee Member for CU Graduate Experiences for Multicultural Students
N/A
N/A
2019
Mentor for CU-Anschutz ISCORE undergraduate mentorship program
N/A
N/A
2019
BioFrontiers Hackathon
N/A
N/A
2018
Data Incubator Data Science Fellowship
N/A
N/A
2017
Harvard Medical School Scientists Teaching Science Course
N/A
N/A
2016
Organizer for UCSD Ethics Center’s Silent Spring Project
N/A
N/A
2012
Dr Huang Memorial Scholarship
N/A
N/A
2011 - 2009
National College Students Creativity Experiment Project
N/A
N/A
2009 - 2007
University Merit Student, First-Class Scholarship
N/A
N/A
2008 - 2006